Jones assisted in the interrogation of Morpheus with his fellow Agents. When Neo and Trinity attempted to rescue Morpheus from the government building where Morpheus was held, Jones materialized in the body of a chopper pilot who was desperately calling for backup. Jones used his extreme speed to dodge Neo's bullets, but failed to kill Neo, who was similarly able to avoid fatal wounds. Trinity shot Jones through the head at close range, saving Neo but merely sending Jones out of the body of the nearest soldier, a helicopter pilot named "Kim ".

His statement towards Neo when he is prepared to kill Neo, "Only Human.", implies that he has a degree of dislike towards Humanity, although not to the extent of Agent Smith.

In The Matrix: Path of Neo, he fights Neo one more time in the part of the game called "Red Pill rescue", along with Agent Brown. Unlike the Upgraded Agents of the next level, he cannot regenerate his health. After the player has rescued all four Red Pills, Jones is never seen again, same for Brown.